text: DNA replication and RNA transcription both make use of base flipping.  DNA polymerase is an enzyme that carries out replication.  It can be thought of as a hand that grips the DNA single strand template.  As the template passes across the palm region of the polymerase, the template bases are flipped out of the helix and away from the dNTP binding site.  During transcription, RNA polymerase catalyzes RNA synthesis.  During the initiation phase, two bases in the -10 element flip out from the helix and into two pockets in RNA polymerase.  These new interactions stabilize the -10 element and promote the DNA strands to separate or melt.
  Base flipping occurs during latter stages of recombination.  RecA is a protein that promotes strand invasion during homologous recombination.  Base flipping has been proposed as the mechanism by which RecA can enable a single strand to recognize homology in duplex DNA.  Other studies indicate that it is also involved in V(D)J Recombination.